Chronic Kidney Disease (CKD) is an independent risk factor for cardiovascular disease (CVD). CKD is accompanied by high cardiovascular mortality due to many factors, but atherosclerosis is thought to be a major cause at every CKD stage. It has been suggested that measuring and estimating changes in high density lipoprotein (HDL) and low density lipoprotein (LDL) subfractions may be important for predicting CVD in CKD patients.The aim of this study was to determine and compare levels of HDL and LDL subfractions in patients with different CKD stages.The study included 115 patients with CKD (CKD stage 2-25 patients, CKD stage 3-25; CKD stage 4-25 and CKD 5 undergoing dialysis - 40 patients) and 25 volunteers without CKD (control group). The Lipoprint System (Quantimetrix®) was used to analyse HDL and LDL subfractions.There were significant differences in the distribution of HDL1-HDL5 subfractions levels, which were significantly higher in patients with impaired renal function than in the control group (p≤.0.013 for all comparisons). HDL7-HDL10 subfractions were significantly more prevalent in healthy volunteers compared with CKD patients (p≤.0.001 for all comparisons). The analysis of LDL subfractions revealed significant differences only in IDL-B (p<0.05), IDL-A (p<0.05) and LDL2 (p<0.001) between patients with CKD stage 5 and controls.CKD influenced HDL and LDL subfractions. In CKD patients, large HDL subpopulations were more prevalent in contrast to small HDL subfractions in healthy subjects. Identification of patients with increased level of large HDL subfractions could be useful to identify CKD subjects at increased CV risk. Further studies with larger populations and with the application of a several methods of subfraction measurement are necessary to confirm these results.